AMBER Archive (2008)

Subject: RE: AMBER: Electrostatic Energy Components

From: Ilyas Yildirim (
Date: Fri Nov 21 2008 - 18:12:44 CST

Dear Ross,

> Note, however that I have seen many times where people try to fit their own
> parameters and they produce a nice QM dihedral profile and then just fit the
> dihedral term to this (forgetting all about including the 1-4 EEL and VDW
> terms as well). Hence what they actually think they have fitted to they have
> not and when they then include it in a large simulation they don't realize
> that their actual force field parameters are bogus since they forgot the 1-4
> contributions.

Thanks for your explanations, but I could not understand this paragraph
of yours. Let's say we have created a nice QM profile of a particular
torsion. To do the fitting, the MM energy without the dihedral energy of
this particular torsion should be calculated (let's call it MM_1). This
means that an frcmod file with zero torsional barrier of the particular
torsion needs to be used. Then, QM-MM_1 is calculated, which is fitted to
the desired cosine terms. If the fitting will include 2 cosine terms, for
example, QM-MM_1 should be fitted to V_1 * (1+cos(n1*x)) + V_2 *

In the whole above process, the 1-4EEL and VDW terms are not
used/calculated explicitly. They are included in the MM_1
energy implicitly. Did you mean that? Thanks.

Best regards,

  Ilyas Yildirim, Ph.D.
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  =                     =

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